Steven Chu: Secret life of molecules 7/16/97

Steven Chu: Uncovering
the secret life of molecules

BY DAVID F. SALISBURY

Ten years ago, while he was working
at AT&T Bell Laboratories, Steven Chu and two of his colleagues
invented a marvelous tool called optical tweezers -- a kind of
microscopic version of Star Trek tractor beams. By specially tuning
a laser beam, the scientists found that they could grip and
manipulate a number of different kinds of microscopic objects
immersed in water, including bacteria.

Since coming to Stanford in 1987,
the physicist has found an interesting way to use the capabilities
of this instrument: studying the physical properties of individual
polymer molecules. In two recently published papers, Chu and his
students have demonstrated that studying polymers one-by-one can
provide important new insights into the way in which the properties
of polymeric materials arise from the collective action of large
numbers of individual molecules.

Polymers are large spaghetti-like
molecules that are constructed from large numbers of identical,
smaller molecules strung together like beads on a string. Polymers
figure in everything from plastics to synthetic fabrics to the DNA
in living cells. Previously, scientists had been limited to
studying polymers in bulk, by the millions and billions. Chu's
laboratory is providing some of the first detailed studies of the
behavior of individual polymers that, not surprisingly, are
revealing that they don't act in exactly the way that scientists
had expected.

Studying the properties of polymers
in bulk is something like trying to determine the nature of animals
in a zoo using only information about averages, Chu explained. "If
someone did a series of experiments that only measured the average
size, weight and number of legs of the animals, he would get a
distorted picture. For example, he might find that the average
number of legs on the animals is 2.7, and then look for a theory of
animal development that could explain his finding. Only by looking
at individual animals can you get a true sense of the diversity of
species."

The study that was published in the
July 10 issue of the journal Nature was conducted with
former student Steven Quake, now an assistant professor of physics
at the California Institute of Technology. He and Chu found that a
single strand of polymer immersed in water obeys the same simple
law of motion as a plucked guitar string. That in itself is not so
surprising, says Chu, but what intrigues him is the remarkable
precision of the molecule's adherence to this 200-year-old law.
Previously, scientists had thought that such molecules would
exhibit much more complex behavior. "We decided to take the analogy
to the guitar string very seriously and see how well it held up. It
turned out to be much closer than we expected," Chu
said.

In the second study, Chu and two
doctoral students also discovered that these molecules appear to
express a surprising degree of individuality. When forced to
unravel in a strong current, apparently identical polymers unwind
in highly individual and unpredictable ways.

Guitar analogy

The idea that the motions of a
polymer can be described by a set of frequencies corresponding to a
fundamental tone and its higher harmonics, similar to the
vibrations of a musical string, is an old one. But most researchers
have considered this simple "linear theory" to be only a rough
description of the actual motion. In the real world, polymers are
submerged in a solution and capable of forming knots, so scientists
have thought that their behavior must be more complex and less easy
to predict.

To study individual polymer
vibrations, the scientists used strands of DNA 20 microns long. (A
strand of human hair is about 25 microns across.) Previous
experiments indicate that DNA strands act as generic polymers. That
is, DNA behaves in the same way as any other polymer in these types
of experiments. It is also readily available, can be labeled with
fluorescent dye, and the researchers in Chu's lab have successfully
developed a method that allows them to securely attach the ends of
DNA to tiny plastic spheres, enabling them to manipulate the
strands using optical tweezers.

For the harmonics study, the
researchers attached the tiny spheres, which are about one-third of
a micron in diameter, to both ends of the DNA molecules. Then,
using a pair of optical tweezers, they gripped the spheres at each
end of a DNA strand and pulled them far enough apart to stretch the
molecules to about three-quarters of their full length.

DNA is too tiny to see with an
optical microscope. But the dyed strands showed up clearly, so the
scientists were able to videotape their vibrations. The thermal
agitation of the water molecules, called Brownian motion, acted
like tiny fingers plucking at the strand. When the researchers
analyzed these movements, they found that they could be described
by the motion of a set of independent harmonic tones to an accuracy
of better than 1 percent. They carried their analysis up to the
eighth harmonic.

Harmonic motion first was described
by the French mathematician D'Alembert in the 1700s. He discovered
that the motion of a string held taut at both ends could be fully
described by superimposing a series of simple sine waves with
wavelengths that fit evenly into its length. In 1954 American
scientist Bruno Zimm suggested that the motion of a polymer in
solution can actually be explained by D'Alembert's mathematical
description.

Normally, a scientist would not even
try to use such a linear theory to describe the movement of a
polymer in solution. If you move one segment of a single strand
that is submerged in water, that movement generates water waves
that then exert forces on all the other segments. The force exerted
on closer segments is greater than that exerted on segments farther
away. Since the distance of the segments depends on the
instantaneous configuration of the entire polymer, the mathematics
to solve this problem becomes intractable.

To simplify the math, Zimm replaced
actual distances between segments with average distances. Strictly
speaking this assumption is not mathematically rigorous. In his
treatment he left out a number of complicated effects: For example,
his model allowed the polymer to pass through itself as a
"phantom-like" strand. Despite the shaky derivation, the basic
conclusion that polymer motions can be described by a linear set of
equations may still be correct, Chu said.

Twenty years later Pierre-Gilles de
Gennes, professor of the Collège de France and winner of the
Nobel Prize for his contributions to polymer science, emphasized
that collective polymer motion was far more complicated than had
been assumed by Zimm and others. As an alternative, he developed a
"scaling" theory that describes the dynamics of a polymer without
having to linearize the equations that describe its
motion.

"Because we can actually see the
molecules move, we can directly observe the higher-order vibrations
for the first time. When we started this work, we sided with de
Gennes and felt that polymer motion cannot be perfectly linear. But
we looked very hard for non-linearity and found no evidence for
it," Chu added. The researchers are continuing their search for a
breakdown of the harmonic model.

How DNA strands unravel

Chu's second study, performed with
graduate students Thomas T. Perkins and Douglas E. Smith, was
published in the June 27 issue of the journal Science.
It shows that identical polymers in identical conditions act quite
differently, indicating that small random conditions play an
unexpectedly important role in the way polymers unravel.

In that experiment Chu and his two
doctoral students observed how immersed DNA strands unravel when
exposed to microscopic currents. Such
currents, or flow fields, occur as a fluid passes through any
constriction or nozzle. Understanding how polymers
deform in these fields is necessary to understand how polymers can
reduce drag in pipelines and how they behave during processes such
as injection molding.

In this case, the researchers did
not use the optical tweezers. Instead, they manufactured
microscopic currents by using microfabrication techniques to etch
perpendicular flow channels only 650 microns wide and 220 microns
deep on a small plate. Fluorescently labeled DNA molecules flowed
down one channel until they reached the center of the cell, where
they moved into a cross-current. The researchers videotaped the
molecules as they reacted to the cross-current by unraveling to a
greater or lesser extent.

Despite taking great care to use
identical strands of DNA in identical flow conditions, the
experimenters observed a great diversity in the way that they
unraveled. "We have found that random thermal fluctuations in the
initial starting point of the elongation get magnified into
dramatic differences in the way each molecule unravels," Chu
said.

Until now theorists have described
the elongation of these molecules according to a "mean-field"
theory that assumes the description of the average behavior is
adequate. Since all the previous polymer experiments probed the
behavior of a large collection of molecules, an average or
so-called "mean-field" theory was developed that fit the
experimental data. The new results indicate that any such
"averaged" theory is incorrect.

Instead, the observation of
thousands of individual molecules showed the researchers that the
elongation process follows a number of different scenarios and the
rate at which they unwind depends greatly on the initial shape of
the partially coiled polymers.

An even more surprising outcome of
the experiment was that even when identically coiled polymers are
exposed to the same currents, they do not behave in the same
fashion. This unpredictable behavior is what de Gennes has called
"molecular individualism." As the Nobel laureate states in a
comment on the Stanford paper in the same issue of Science,
"Normally, the average coil shape is enough to describe many
features. But not here."

This individualism apparently arises
from small random conditions. "We have found that random thermal
fluctuations in the initial starting point of the elongation get
magnified into dramatic differences in the way each molecule
unravels," Chu said. "In the 'nature versus nurture' debate, no one
pays attention to the importance of tiny random influences. Perhaps
such influences play an important role in how our lives evolve as
well." SR